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8,338 results for “methylation”
Maternal Glycemic Dysregulation During Pregnancy and Neonatal Blood DNA Methylation: Meta-analyses of Epigenome-Wide Association Studies
<p>Maternal glycemic dysregulation during pregnancy increases the risk of adverse health outcomes in her offspring, a risk thought to be linearly related to maternal hyperglycemia. It is hypothesized that changes in offspring DNA methylation (DNAm) underline these associations. To address this hypothesis, we conducted fixed-effects meta-analyses of epigenome-wide association study (EWAS) results from eight birth cohorts investigating relationships between cord blood DNAm and fetal exposure to maternal glucose (Nmaximum= 3,503), insulin (Nmaximum= 2,062), and area under the curve of glucose (AUCgluc) following oral glucose tolerance tests (Nmaximum = 1,505). Inflation and bias was addressed with the bacon Bioconductor package for individual cohorts and the meta-analysis results and reported model estimates and standard errors are adjusted. Greater maternal AUCgluc during pregnancy was associated with lower cord blood DNAm at neighboring CpGs cg26974062 and cg02988288 in TXNIP. Follow-up analyses show that these changes may have functional and later-life consequences and warrant further mediation and causal analysis. </p> <p>The corresponding paper can be found here: https://doi.org/10.2337/dc21-1701.</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a Zenodo DOI generated for you go to ewascatalog.org/upload.</p>
Genome-wide DNA methylation profiling identifies epigenetic signatures of β-lactams induced fatal anaphylactic shock
<p>Drug hypersensitivity is one of the most frequent causes of anaphylaxis in adults, of which antibiotics are the most common culprits, particularly β-lactams induced anaphylactic shock deaths. We provided the genome wide DNA methylation profiling study of PBMC from 14 individuals peripheral venous blood samples. Illumina Infinium Human Methylation EPIC BeadChip was used. Among the 14 individuals, 8 patients were died from β-lactams induced anaphylactic shock, 6 healthy individuals were controls. Inclusion criteria for the β-lactams induced anaphylactic shock as follows: ①A clear history of β-lactams transfusion or components of β-lactams detected from blood (or skin of suspicious infusion site); ②Shock symptoms occurred after infusion of β-lactams and died within a short period of time; ③The immunohistochemical results of throat, lung and gastrointestinal tissues showed that tryptase or chymase were mostly positive expression; ④ Excluding other causes (disease, poisoning) of death; ⑤ No decay occurred in the corpse.Inclusion criteria for controls as follows: ① Healthy, no previous common underlying diseases and no history of genetic disease; ② No history of allergies to drugs, food, pollen and so on; ③Skin prick test (SPT) is negative, allergen-specific IgE (sIgE)< 100IU/mL; the skin test results of β-lactam drugs were negative.</p>
NMR assignment of methyl groups in solid-state using 1H-detection and fast MAS - NMR raw and processed data
<p>This data set contains raw NMR data in Bruker format for experimental series on (1) 2,3-13C-labelled microcrystalline alanine, (2) U-13C,15N-labelled N-fomylated microcrystalline tripeptide Met-Leu-Phe, and (3,4) two differently labelled (ILV-C4 and ILV-C5) microcrystalline chicken-alpha-spectrin SH3 domain. Measurements were performed at 14.4 T and 55.5 kHz MAS (alanine), 18.8 T and 55.5 and 98 kHz MAS (fMLF), 23.5 T and 55.5 kHz (SH3 C5), 18.8T and 55.5 and 94.5 kHz MAS (SH3 C5) and 18.8T and 55.5 and 94.5 kHz MAS (SH3 C4). The data set also contains Fourier processed data (spectra) in UCSF format, Sparky project, save and peak list files. Pulse programs for Bruker spectrometers are provided. The data set is complemented with SIMPSON scripts for simulation of spin dynamics under aformentioned conditions.</p>
Gigantic genomes of salamanders indicate body temperature, not genome size, is the driver of global methylation and 5-methylcytosine deamination in vertebrates
<p>Transposable elements (TEs) are sequences that replicate and move throughout genomes, and they can be silenced through methylation of cytosines at CpG dinucelotides. TE abundance contributes to genome size, but TE silencing variation across genomes of different sizes remains underexplored. Salamanders include most of the largest C-values -- 9 to 120 Gb. We measured CpG methylation levels in salamanders with genomes ranging from 2N = ~58 Gb to 4N = ~116 Gb. We compared these levels to results from endo- and ectothermic vertebrates with more typical genomes. Salamander methylation levels are ~90%, higher than all endotherms. However, salamander methylation does not differ from other ectotherms, despite a ~100-fold difference in nuclear DNA content. Because methylation affects the nucleotide compositional landscape through 5-methylcytosine deamination to thymine, we quantified salamander CpG dinucleotide levels and compared them to other vertebrates. Salamanders and other ectotherms have comparable CpG levels, and ectotherm levels are higher than endotherms. These data show no shift in global methylation at the base of salamanders, despite a dramatic increase in TE load and genome size. This result is reconcilable with previous studies by considering endothermy and ectothermy, which may be more important drivers of methylation in vertebrates than genome size.</p>
MeDeMo - a dependency model for DNA methylation-aware transcription factor binding predictions
<p>The uploaded <em>fasta </em>files contain extended reference genomes for three cell lines HepG2, GM12878, K562 (ENCODE) and two primary liver hepatocyte samples from the german epigenomics consortium (DEEP). The extended reference genomes contain information on DNA methylation in a CpG context. They can be used as input for <em>MeDeMo</em>, a tool to infer transcription factor binding sites incorporating not only sequence specificity but also DNA methylation. <em>MeDeMo </em>is available online at: <a href="http://www.jstacs.de/index.php/MeDeMo">http://www.jstacs.de/index.php/MeDeMo</a>.</p> <p>We considered the files ENCFF279HCL and ENCFF835NTC for GM12878, ENCFF867JRG and ENCFF721JMB for K562 as well as ENCFF064GJQ and ENCFF369YQW for HepG2. From DEEP, we considered samples 41_Hf01 and 41_Hf03 which are available through the International Human Epigenomics Consortium (IHEC).</p> <p>In addition, we provide all models trained using the mentioned data sets as well models for and motifs from genome wide predictions.</p>
Acute lymphoblastic leukemia displays a distinct highly methylated genome (source data)
<p>DNA methylation is tightly regulated during development and is stably maintained in normal cells. In contrast, the methylome of cancer cells is commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data examining large cohorts at genome-wide scale are lacking. Here, we performed whole genome bisulfite sequencing (WGBS) of leukemic cells of multiple subtypes of ALL, leukemia cell lines and normal hematopoietic cells, and show that in contrast to most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T-ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands across patients that is influenced by TET2 and DNMT3B. These findings demonstrate a distinct methylome of ALL characterized by an unusually highly methylated genome, and provide important insights into the mechanisms underlying deregulation of methylation in cancer.</p>
Residential greenness-related DNA methylation changes
<p>EWAS of residential greenness in the population-representative Swiss samples.</p> <p>EWAS of two different residential greeness are included here: </p> <ul> <li>NDVI of 500 m circular buffer surrounding residential address (ewas_final_truncate_green500.csv)</li> <li>NDVI of 30x30m cell surrounding residential address (ewas_final_truncate_green30.csv)</li> </ul> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a Zenodo DOI generated for you go to ewascatalog.org/upload.</p> <p> </p>
Investigating the DNA methylation profile of e-cigarette use
<p>EWAS of smoking (vs. non-smoking) in SEE-Cigs study (smvsnon_mainmodel.csv)</p> <p>EWAS of e-cigarette use (vs. smoking) in SEE-Cigs study (vapevssm_mainmodel.csv)</p> <p>EWAS of e-cigarette use (vs. non-smoking) in SEE-Cigs study (vapevsnon_mainmodel.csv)</p>
Maternal Dietary Glycemic Index and Glycemic Load in Pregnancy and Offspring Cord Blood DNA Methylation
<p><strong>Abstract</strong></p> <p><strong>Objective</strong>: Suboptimal nutrition in pregnancy is associated with worse offspring cardiometabolic health. DNA methylation may be an underlying mechanism. We meta-analyzed epigenome-wide association studies (EWASs) of maternal dietary glycemic index and load with cord blood DNA methylation.</p> <p><strong>Research Design and Methods</strong>: We calculated maternal glycemic index and load from food frequency questionnaires, and ran EWASs on cord blood DNA methylation in 2003 mother-offspring pairs from three cohorts. Analyses were additionally stratified by maternal BMI categories. We looked-up the findings in EWASs of maternal glycemic traits and BMI, and in EWASs of birthweight and child BMI. We examined associations with gene expression in child blood in the online Human Early Life Exposome eQTM catalogue and in 223 adipose tissue samples.</p> <p><strong>Results</strong>: Maternal glycemic index and load were associated with cord blood DNA methylation at 41 cytosine-phosphate-guanine sites (CpGs, P<1.17x10<sup>-7</sup>), mostly in mothers with overweight/obesity. We did not observe overlap with CpGs associated with maternal glycemic traits, BMI or child birthweight or BMI. Only DNA methylation at cg24458009 and cg23347399 was associated with expression of <em>PCED1B</em> and <em>PCDHG</em>, respectively, in child blood, and DNA methylation at cg27193519 was associated with expression of <em>TFAP4</em>, <em>ZNF500</em>, <em>PPL</em> and <em>ANKS3</em> in child subcutaneous adipose tissue.</p> <p><strong>Conclusions</strong>: We observed multiple associations of maternal glycemic index and load during pregnancy with cord blood DNA methylation, mostly in mothers with overweight/obesity; some of these CpGs were associated with gene expression. Additional studies are required to further explore functionality, uncover causality, and study pathways to offspring health.</p>
Elucidation of radical- and oxygenate-driven paths in zeolite-catalyzed conversion of methanol and methyl chloride to hydrocarbons
<p>Dataset corresponding to the publication:</p> <p><strong>Elucidation of radical- and oxygenate-driven paths in zeolite-catalyzed conversion of methanol and methyl chloride to hydrocarbons</strong></p> <p>Alessia Cesarini,<sup>1†</sup> Sharon Mitchell,<sup>1†</sup> Guido Zichittella,<sup>1†</sup>* Mikhail Agrachev,<sup>2</sup> Stefan P. Schmid,<sup>2</sup> Gunnar Jeschke,<sup>2</sup> Zeyou Pan,<sup>3</sup> Andras Bodi,<sup>3</sup> Patrick Hemberger,<sup>3</sup>* and Javier Pérez‑Ramírez<sup>1</sup>*</p> <p><sup>1</sup> Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland,</p> <p><sup>2</sup> Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland,</p> <p><sup>3</sup> Laboratory of Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland,</p> <p><sup>†</sup>These authors contributed equally, listed alphabetically.</p> <p>*Corresponding author. E-mails: zguido@mit.edu, <a href="mailto:patrick.hemberger@psi.ch">patrick.hemberger@psi.ch</a>, jpr@chem.ethz.ch.</p>
Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), ATXN1, SLC17A6, NR4A2, and PTPRN2 in cortical neurons
<p>Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell-type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this first genome-wide analysis of DNA methylation in an enriched neuronal population from PD post-mortem parietal cortex, we report sex-specific PD-associated methylation changes in <em>PARK7</em> (DJ-1), <em>SLC17A6</em> (VGLUT2), <em>PTPRN2</em> (IA-2β), <em>NR4A2</em> (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.</p>
Code and data for "Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer".
<p>Code and data for "<strong>Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer</strong>".</p> <ul> <li> <p>The publicly available datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository (<a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a>) and UCSC Xena Browser (TCGA, <a href="https://xena.ucsc.edu/">https://xena.ucsc.edu/</a>).</p> </li> </ul>
BETA values from DNA methylation (selected differential regions)
<p><span>Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the "biologically embedding" of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation 850K BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with, versus those without, neglectful behavior (n = 51 vs 87) that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the </span><span>α</span><span> = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development, and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and Alzheimer's disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.</span></p>
Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models (NMR datasets, maternal plasma and infant brain)
<p>Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. Ultimately, maternal obesity altered infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors. </p>
Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination
<p>Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (<em>Alligator mississippiensis</em>), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and 4 test samples) and past incubation temperature with a mean absolute error of 1.2˚C (in 4 test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity. </p>
Non-euryarchaeotal methyl-coenzyme M reductase, alpha subunit (McrA) genes
<p>Protein sequences of the non-euryarchaeotal methyl-coenzyme M reductase, alpha subunit (McrA) genes reported in:</p> <p>Evans PN, et al. 2015. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 350, 434-8.</p> <p>doi: 10.1126/science.aac7745.</p> <p>PMID: 26494757</p> <p> </p>
Supporting data for "Charging Poly(methyl Methacrylate) Latexes in Nonpolar Solvents: Effect of Particle Concentration" (Langmuir, doi:10.1021/acs.langmuir.7b02257)
<p>Raw data:</p> <p>- Electrophoretic mobilities as a function of particle concentration (Volume fraction phi [unitless, volume per volume], mu [m^2/(V s)], error mu [m^2/(V s]).</p> <p>- Small-angle neutron scattering curves (Q [1/Å], I(Q) [1/cm], error I(Q) [1/cm]).</p> <p>- Small-angle X-ray scattering curves (Q [1/Å], I(Q) [unitless, instrument intensity divided by fit scale]).</p>
Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes
<p>Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. <em>Eragrostis curvula</em> is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in <em>E</em>. <em>curvula</em> genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.</p>
Differential methylation patterns in apomictic vs. sexual genotypes of the diplosporous grass Eragrostis curvula.
<p>Methylation is an epigenetic mechanism where a methyl group take place over the C5 of cytosine or C6 of adenine repressing or de-repressing genes depending on the context, position (coding or non-coding) and species. Eragrostis curvula is a forage grass that reproduces by apomixis. Increases of the frequency of sexual pistils in facultative genotypes of this grass has been associated to epigenetic changes triggered by different biotic and abiotic stresses. The aim of the present study was to associate differences in the reproductive mode with specific methylated regions and genes contrasting full apomictic, facultative and sexual genotypes using the methylation sensitive technique MCSeEd. The distribution of the differentially methylated positions over the genes shows a peak around the start and stop codon boundaries, hence regulating gene expression mainly through the incorporation of methyl groups on these positions. The main pathways being regulated were ubiquitin and auxins. The methylation pathway itself was also found to be self-regulated since ROS1 and ROS4, the main demethylating genes were found differentially methylated among the different genotypes. Even more, this work allowed us to detect genes regulated by methylation that were previously found differentially expressed in the comparisons between apomictic and sexual genotypes.</p>
Methylation profiling of Waldenstorm's Macroglobulinemia
<p><span>Currently, the role of DNA methylation in the IgM-monoclonal gammopathy disease spectrum remains poorly understood. In the present study, a multi-omics prospective analysis was conducted integrating DNA methylation, RNA-seq and WES data in 34 subjects [23 WM, 6 IgM-MGUS, 5 normal controls]. Analysis was focused on defining differences between IgM-gammopathies (WM/IgM-MGUS) compared to controls, and specifically between WM and IgM-MGUS. Between groups, genome-wide DNA methylation analysis demonstrated a significant number of differentially methylated regions which were annotated according to genomic region. Next, integration of RNA-seq data was performed to identify potentially epigenetically deregulated pathways. We found that pathways involved in cell cycle, metabolism, cytokine/immune signaling, cytoskeleton, tumor microenvironment, and intracellular signaling were differentially activated and potentially epigenetically regulated. Importantly, there was a positive enrichment of CXCR4 signaling pathway along with several interleukin (IL-6, IL-8, IL15) signaling pathways in WM compared to IgM-MGUS. Further assessment of known tumor suppressor genes and oncogenes uncovered differential promoter methylation of several targets with concordant change in gene expression, including <em>CCND1</em> and <em>CD79B</em>. Overall, this report define how aberrant DNA methylation in IgM-gammopathies may play acritical role in the epigenetic control of oncogenesis and key cellular functions. </span></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.